Abstract

Background

The Firmicutes often possess three conspicuous genome features: marked Purine Asymmetry
(PAS) across two strands of replication, Strand-biased Gene Distribution (SGD) and
presence of two isoforms of DNA polymerase III alpha subunit, PolC and DnaE. Despite
considerable research efforts, it is not clear whether the co-existence of PAS, PolC
and/or SGD is an essential and exclusive characteristic of the Firmicutes. The nature
of correlations, if any, between these three features within and beyond the lineages
of Firmicutes has also remained elusive. The present study has been designed to address
these issues.

Results

A large-scale analysis of diverse bacterial genomes indicates that PAS, PolC and SGD
are neither essential nor exclusive features of the Firmicutes. PolC prevails in four
bacterial phyla: Firmicutes, Fusobacteria, Tenericutes and Thermotogae, while PAS
occurs only in subsets of Firmicutes, Fusobacteria and Tenericutes. There are five
major compositional trends in Firmicutes: (I) an explicit PAS or G + A-dominance along
the entire leading strand (II) only G-dominance in the leading strand, (III) alternate
stretches of purine-rich and pyrimidine-rich sequences, (IV) G + T dominance along
the leading strand, and (V) no identifiable patterns in base usage. Presence of strong
SGD has been observed not only in genomes having PAS, but also in genomes with G-dominance
along their leading strands – an observation that defies the notion of co-occurrence
of PAS and SGD in Firmicutes. The PolC-containing non-Firmicutes organisms often have
alternate stretches of R-dominant and Y-dominant sequences along their genomes and
most of them show relatively weak, but significant SGD. Firmicutes having G + A-dominance
or G-dominance along LeS usually show distinct base usage patterns in three codon
sites of genes. Probable molecular mechanisms that might have incurred such usage
patterns have been proposed.

Conclusion

Co-occurrence of PAS, strong SGD and PolC should not be regarded as a genome signature
of the Firmicutes. Presence of PAS in a species may warrant PolC and strong SGD, but
PolC and/or SGD not necessarily implies PAS.